[gmx-users] about the traj modification

zh.li zh.li at jacobs-university.de
Thu Jan 14 17:10:08 CET 2010

Dear Justin,
     Thanks for your instant reply about my problem. I've already
finished the make_ndx part, choosing the "protein" option. But for
trjconv, how can I write the command line to have the prompt "Select
group for output"? Sorry, I'm really a beginner. Thank you!


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: 2010年1月13日 0:21
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the traj modification

zh.li wrote:
> Dear all,
>      I want to remove the water molecules in the original traj file 
> (run.xtc) to save the space, so that I should use the command
> But I don’t know which sub-command I should use to realize that? Does

> anyone here know how to do it? Thank you very much.

You'll need an index group that defines all non-solvent atoms (easily
done with 
make_ndx).  Pass the index file to trjconv and simply choose your
group when prompted "Select group for output."


> Zhenwei Li


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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